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PEDS Advance Access published online on March 24, 2006
Protein Engineering Design and Selection, doi:10.1093/protein/gzl009
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org
Received October 18, 2005
Revised February 1, 2006
Accepted February 21, 2006

Article

A simple approach for protein structure discrimination based on the network pattern of conserved hydrophobic residues

Usha K. Muppirala 1 and Zhijun Li 2 *

1 Bioinformatics Program, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA
2 Bioinformatics Program, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA; Department of Chemistry & Biochemistry, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA

* To whom correspondence should be addressed.
Zhijun Li, E-mail: z.li{at}usip.edu


  Abstract

Evolutionarily conserved hydrophobic residues at the core of protein structures are generally assumed to play a structural role in protein folding and stability. Recent studies have implicated that their importance to protein structures is uneven, with a few of them being crucial and the rest of them being secondary. In this work, we explored the possibility of employing this feature of native structures for discriminating non-native structures from native ones. First, we developed a network tool to quantitatively measure the structural contributions of individual amino acid residues. We systematically applied this method to diverse fold-type sets of native proteins. It was confirmed that this method could grasp the essential structural features of native proteins. Next, we applied it to a number of decoy sets of proteins. The results indicate that such an approach indeed identified non-native structures in most test cases. This finding should be of help for the investigation of the fundamental problem of protein structure prediction.

Keywords: connectivity pattern; conserved hydrophobic residue; hub-residue; network; protein structure.
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